RPS-BLAST 2.2.22 [Sep-27-2009] Database: pdb70 24,244 sequences; 5,693,230 total letters Searching..................................................done Query= gi|254780474|ref|YP_003064887.1| ubiquinol oxidase, subunit II [Candidatus Liberibacter asiaticus str. psy62] (332 letters) >1fft_B Ubiquinol oxidase; electron transport, cytochrome oxidase, membrane protein, oxidoreductase; HET: HEM HEO; 3.50A {Escherichia coli} SCOP: b.6.1.2 f.17.2.1 Length = 315 Score = 296 bits (759), Expect = 5e-81 Identities = 132/309 (42%), Positives = 189/309 (61%), Gaps = 11/309 (3%) Query: 14 KSLKFFFLFFSSVMLSGFEFIVMDPYGDIALQQASLIRIAVALMLLIVVPVFFSILFFAW 73 KSL + LF +V+LSG ++DP G I L+Q SLI A LML++V+P + FAW Sbjct: 8 KSLGWLSLFAGTVLLSGCNSALLDPKGQIGLEQRSLILTAFGLMLIVVIPAILMAVGFAW 67 Query: 74 KYRSTNKKARYDPKWCHSTLLELFVWLVPLVIVGFLAVITWDATHRMDPYAPLERISESK 133 KYR++NK A+Y P W HS +E VW VP++I+ FLAV+TW TH ++P PL Sbjct: 68 KYRASNKDAKYSPNWSHSNKVEAVVWTVPILIIIFLAVLTWKTTHALEPSKPL------- 120 Query: 134 SIAKNSKPLVVEVVALDWKWLFLLPEQQVAIINELVVPIDRPLEFRITASSVMNSFYIPG 193 A + KP+ +EVV++DWKW F+ PEQ +A +NE+ P + P+ F++T++SVMNSF+IP Sbjct: 121 --AHDEKPITIEVVSMDWKWFFIYPEQGIATVNEIAFPANTPVYFKVTSNSVMNSFFIPR 178 Query: 194 LAGQIYAMAGMETKLHAVMNKKGAYSGFSANYSGRGFSHMRFKFYGKS-EKGFEDWISKV 252 L QIYAMAGM+T+LH + N+ G Y G SA+YSG GFS M+FK F+ W++K Sbjct: 179 LGSQIYAMAGMQTRLHLIANEPGTYDGISASYSGPGFSGMKFKAIATPDRAAFDQWVAKA 238 Query: 253 KRQG-TFLNRQEYLLLKKPSERDSVRYFSPIEKGLYYSILNLCVHPGKICMDEMMRIDAL 311 K+ T + + L PSE + V YFS ++ L+ ++N + GK + Sbjct: 239 KQSPNTMSDMAAFEKLAAPSEYNQVEYFSNVKPDLFADVINKFMAHGKSMDMTQPEGEHS 298 Query: 312 GGGGMRGID 320 GM G+D Sbjct: 299 AHEGMEGMD 307 >1cyx_A CYOA; electron transport; 2.30A {Escherichia coli} SCOP: b.6.1.2 PDB: 1cyw_A Length = 205 Score = 165 bits (419), Expect = 1e-41 Identities = 76/206 (36%), Positives = 115/206 (55%), Gaps = 11/206 (5%) Query: 117 THRMDPYAPLERISESKSIAKNSKPLVVEVVALDWKWLFLLPEQQVAIINELVVPIDRPL 176 TH ++P PL + KP+ +EVV++DWKW F+ PEQ +A +NE+ P + P+ Sbjct: 1 THALEPSKPLAH---------DEKPITIEVVSMDWKWFFIYPEQGIATVNEIAFPANTPV 51 Query: 177 EFRITASSVMNSFYIPGLAGQIYAMAGMETKLHAVMNKKGAYSGFSANYSGRGFSHMRFK 236 F++T++SVM+SF+IP L QIYAMAGM+T+LH + N+ G Y G A G G S M+FK Sbjct: 52 YFKVTSNSVMHSFFIPRLGSQIYAMAGMQTRLHLIANEPGTYDGICAEICGPGHSGMKFK 111 Query: 237 FYG-KSEKGFEDWISKVKRQG-TFLNRQEYLLLKKPSERDSVRYFSPIEKGLYYSILNLC 294 F+ W++K K+ T + + L PSE + V YFS ++ L+ ++N Sbjct: 112 AIATPDRAAFDQWVAKAKQSPNTMSDMAAFEKLAAPSEYNQVEYFSNVKPDLFADVINKF 171 Query: 295 VHPGKICMDEMMRIDALGGGGMRGID 320 + GK + GM G+D Sbjct: 172 MAHGKSMDMTQPEGEHSAHEGMEGMD 197 >3hb3_B Cytochrome C oxidase subunit 2; electron transfer, proton transfer, proton pumping, membrane protein, cell inner membrane, cell membrane, copper; HET: HEA LDA LMT; 2.25A {Paracoccus denitrificans} PDB: 1ar1_B* 3ehb_B* 1qle_B* Length = 298 Score = 123 bits (309), Expect = 6e-29 Identities = 42/241 (17%), Positives = 93/241 (38%), Gaps = 39/241 (16%) Query: 37 DPYGDIALQQASLIRIAVALMLLIVVPVFFSILFFAWKYRSTNKKARYDPKWCHSTLLEL 96 +A Q L + ++ + + V +L ++ + ++ H+T +E+ Sbjct: 51 PASSPLAHDQQWLDHFVLYIITAVTIFVCLLLLICIVRFN--RRANPVPARFTHNTPIEV 108 Query: 97 FVWLVPLVIVGFLAVITWDATHRMDPYAPLERISESKSIAKNSKPLVVEVVALDWKWLF- 155 LVP++I+ + + R N LV++ + W W + Sbjct: 109 IWTLVPVLILVAIGAFSLPILFRSQEM-------------PNDPDLVIKAIGHQWYWSYE 155 Query: 156 -----------------------LLPEQQVAIINELVVPIDRPLEFRITASSVMNSFYIP 192 E +A N +VVP+ + + ++TA+ V++++ IP Sbjct: 156 YPNDGVAFDALMLEKEALADAGYSEDEYLLATDNPVVVPVGKKVLVQVTATDVIHAWTIP 215 Query: 193 GLAGQIYAMAGMETKLHAVMNKKGAYSGFSANYSGRGFSHMRFKFYGKSEKGFEDWISKV 252 A + A+ G +L ++++G Y G + G ++M S++ +E W++ Sbjct: 216 AFAVKQDAVPGRIAQLWFSVDQEGVYFGQCSELCGINHAYMPIVVKAVSQEKYEAWLAGA 275 Query: 253 K 253 K Sbjct: 276 K 276 >2gsm_B Cytochrome C oxidase subunit 2; transmembrane protein complex, oxidoreductase; HET: DMU HEA TRD; 2.00A {Rhodobacter sphaeroides} SCOP: b.6.1.2 f.17.2.1 PDB: 3dtu_B* 3fye_B* 3fyi_B* 1m56_B* 1m57_B* Length = 262 Score = 104 bits (260), Expect = 3e-23 Identities = 41/237 (17%), Positives = 85/237 (35%), Gaps = 22/237 (9%) Query: 37 DPYGDIALQQASLIRIAVALMLLIVVPVFFSILFFAWKYR-STNKKARYDPKWCHSTLLE 95 +A Q L + ++ I + V IL+ W++ NK + Sbjct: 20 PSASPVATQIHWLDGFILVIIAAITIFVTLLILYAVWRFHEKRNKVPARFTHNSPLEIAW 79 Query: 96 LFVWLVPLVIVGFLAVITWDATHRMDP-----------------YAPLERISESKSIAKN 138 V +V LV +G ++ + Y E ES I Sbjct: 80 TIVPIVILVAIGAFSLPVLFNQQEIPEADVTVKVTGYQWYWGYEYPDEEISFESYMIGSP 139 Query: 139 S----KPLVVEVVALDWKWLFLLPEQQVAIINELVVPIDRPLEFRITASSVMNSFYIPGL 194 + + EV + + E +A +VVP+++ + ++T + V++S+ +P Sbjct: 140 ATGGDNRMSPEVEQQLIEAGYSRDEFLLATDTAMVVPVNKTVVVQVTGADVIHSWTVPAF 199 Query: 195 AGQIYAMAGMETKLHAVMNKKGAYSGFSANYSGRGFSHMRFKFYGKSEKGFEDWISK 251 + A+ G +L ++G + G + G ++M SE+ + W+ + Sbjct: 200 GVKQDAVPGRLAQLWFRAEREGIFFGQCSELCGISHAYMPITVKVVSEEAYAAWLEQ 256 >1v54_B Cytochrome C oxidase polypeptide II; oxidoreductase; HET: FME TPO HEA TGL PGV CHD CDL PEK PSC DMU; 1.80A {Bos taurus} SCOP: b.6.1.2 f.17.2.1 PDB: 1oco_B* 1occ_B* 1ocz_B* 1ocr_B* 1v55_B* 2dyr_B* 2dys_B* 2eij_B* 2eik_B* 2eil_B* 2eim_B* 2ein_B* 2occ_B* 2zxw_B* Length = 227 Score = 89.6 bits (222), Expect = 8e-19 Identities = 35/217 (16%), Positives = 74/217 (34%), Gaps = 42/217 (19%) Query: 56 LMLLIVVPVFFSILFFAWKYRSTNKKARYDPKWCHSTLLELFVWLVPLVIVGFLAVITWD 115 ++ LI V + I + +E ++P +I+ +A+ + Sbjct: 30 IVFLISSLVLYIISLMLTTKL-------THTSTMDAQEVETIWTILPAIILILIALPSLR 82 Query: 116 ATHRMDPYAPLERISESKSIAKNSKPLVVEVVALDWKW---------------------L 154 + MD N+ L V+ + W W L Sbjct: 83 ILYMMDEI--------------NNPSLTVKTMGHQWYWSYEYTDYEDLSFDSYMIPTSEL 128 Query: 155 FLLPEQQVAIINELVVPIDRPLEFRITASSVMNSFYIPGLAGQIYAMAGMETKLHAVMNK 214 + + + N +V+P++ + +++ V++S+ +P L + A+ G + + ++ Sbjct: 129 KPGELRLLEVDNRVVLPMEMTIRMLVSSEDVLHSWAVPSLGLKTDAIPGRLNQTTLMSSR 188 Query: 215 KGAYSGFSANYSGRGFSHMRFKFYGKSEKGFEDWISK 251 G Y G + G S M K FE W + Sbjct: 189 PGLYYGQCSEICGSNHSFMPIVLELVPLKYFEKWSAS 225 >1xme_B Cytochrome C oxidase polypeptide II; cytochrome oxidase, heme, heme-AS, integral membrane protein, oxidoreductase; HET: BNG HEM HAS; 2.30A {Thermus thermophilus} SCOP: b.6.1.2 f.17.2.1 PDB: 1ehk_B* 2qpd_B* 2qpe_B* 3bvd_B* 3eh5_B* 3eh3_B* 3eh4_B* Length = 168 Score = 84.0 bits (207), Expect = 4e-17 Identities = 25/179 (13%), Positives = 58/179 (32%), Gaps = 31/179 (17%) Query: 74 KYRSTNKKARYDPKWCHSTLLELFVWLVPLVIVGFLAVITWDATHRMDPYAPLERI---- 129 ++++ Y+ W + ++ F+A+I + P ++ Sbjct: 4 EHKAHKAILAYEKGW---------LAFSLAMLFVFIALIAYTLATHTAGVIPAGKLERVD 54 Query: 130 ----------SESKSIAKNSKPLVVEVVALDWKWLFLLPEQQVAIINELVVPIDRPLEFR 179 ++ + P V L + + + N + VP + F+ Sbjct: 55 PTTVRQEGPWADPAQAVVQTGPNQYTVYVLAFAFGYQP--------NPIEVPQGAEIVFK 106 Query: 180 ITASSVMNSFYIPGLAGQIYAMAGMETKLHAVMNKKGAYSGFSANYSGRGFSHMRFKFY 238 IT+ V++ F++ G + + G + + + G Y Y G G +M Sbjct: 107 ITSPDVIHGFHVEGTNINVEVLPGEVSTVRYTFKRPGEYRIICNQYCGLGHQNMFGTIV 165 >2cua_A Protein (CUA); CUA center, electron transport; 1.60A {Thermus thermophilus} SCOP: b.6.1.2 PDB: 2fwl_B* Length = 135 Score = 70.5 bits (172), Expect = 5e-13 Identities = 26/134 (19%), Positives = 48/134 (35%), Gaps = 21/134 (15%) Query: 116 ATHR--MDPYAPLERI-----------SESKSIAKNSKPLVVEVVALDWKWLFLLPEQQV 162 ATH + P LER+ ++ + P V L + + + Sbjct: 5 ATHTAGVIPAGKLERVDPTTVRQEGPWADPAQAVVQTGPNQYTVYVLAFAFGY------- 57 Query: 163 AIINELVVPIDRPLEFRITASSVMNSFYIPGLAGQIYAMAGMETKLHAVMNKKGAYSGFS 222 N + VP + F+IT+ V++ F++ G + + G + + + G Y Sbjct: 58 -QPNPIEVPQGAEIVFKITSPDVIHGFHVEGTNINVEVLPGEVSTVRYTFKRPGEYRIIC 116 Query: 223 ANYSGRGFSHMRFK 236 Y G G +M Sbjct: 117 NQYCGLGHQNMFGT 130 >1oqw_A Fimbrial protein; type IV pilin, fiber-forming protein, adhesion, pseudomonas aerugionosa, PAK pilin, cell adhesion; 2.00A {Pseudomonas aeruginosa} SCOP: d.24.1.1 Length = 144 Score = 30.2 bits (67), Expect = 0.64 Identities = 14/62 (22%), Positives = 23/62 (37%), Gaps = 7/62 (11%) Query: 92 TLLELFVWLVPLVIVGFLAVITWDATHRMDPYAPLERISESKSIAKNSKPLVVEVVALDW 151 TL+EL ++ + I+G LA I A + Y + + + K VE Sbjct: 2 TLIEL---MIVVAIIGILAAI---AIPQYQNYVARSEGASALASVNPLK-TTVEEALSRG 54 Query: 152 KW 153 Sbjct: 55 WS 56 >1kzy_C Tumor suppressor P53-binding protein 1; tandem-BRCT and linker complexed with non-BRCT protein, three-helix bundle, parallel beta sheet; 2.50A {Homo sapiens} SCOP: c.15.1.4 c.15.1.4 PDB: 1gzh_B Length = 259 Score = 27.4 bits (60), Expect = 4.4 Identities = 11/70 (15%), Positives = 21/70 (30%), Gaps = 1/70 (1%) Query: 246 EDWISKVKRQGTFLNRQEYLLLKKPSERDSVRYFSPIEKGLYYSILNLCVHPG-KICMDE 304 W+ N + YLL S + + + ++ L V + ++ Sbjct: 115 HVWVHDSCHANQLQNYRNYLLPAGYSLEEQRILDWQPRENPFQNLKVLLVSDQQQNFLEL 174 Query: 305 MMRIDALGGG 314 I GG Sbjct: 175 WSEILMTGGA 184 >1oxw_A Patatin; alpha/beta class fold with approximately three layers; 2.20A {Solanum cardiophyllum} SCOP: c.19.1.3 Length = 373 Score = 26.8 bits (58), Expect = 7.2 Identities = 8/18 (44%), Positives = 14/18 (77%) Query: 302 MDEMMRIDALGGGGMRGI 319 + EM+ + ++ GGG+RGI Sbjct: 12 LGEMVTVLSIDGGGIRGI 29 Database: pdb70 Posted date: Jan 26, 2011 11:21 AM Number of letters in database: 5,693,230 Number of sequences in database: 24,244 Lambda K H 0.326 0.141 0.437 Gapped Lambda K H 0.267 0.0486 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 24244 Number of Hits to DB: 3,010,336 Number of extensions: 138639 Number of successful extensions: 433 Number of sequences better than 10.0: 1 Number of HSP's gapped: 422 Number of HSP's successfully gapped: 27 Length of query: 332 Length of database: 5,693,230 Length adjustment: 93 Effective length of query: 239 Effective length of database: 3,438,538 Effective search space: 821810582 Effective search space used: 821810582 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 57 (26.3 bits)